I am a new user and I have this old issue again with my fresh Ver9 installation. I searched the forum topics but as far as I could see the thread that was started last year did not have any solution to this problem.
To make it more complicated this issue is quite random. Sometimes everything is OK and the next hour no folders and files. After waiting for one or two hours suddenly everything starts working again perfectly.
My installation is hosted on a Siteground Cloud Plan. Those guys are really good in what they are doing. I informed them about this problem and they experienced the same erratic thing. They watched the behavior of the script for half a day but no error message was generated at any level.
Anything that could help?